When war came, Jackson rose to prominence and earned his nickname after the first battle of Bull Run in July 1861, where his brigade was said to "stand like a stone wall" against the Union assault. He was quickly promoted to divisional command.

In May and June of 1862, he was given an independent command in the Shenandoah Valley[?]. There he soundly thrashed the Union forces in a series of battles, showing great audacity, excellent knowledge and shrewd usage of the terrain, and the ability to inspire his troops to great feats of marching and fighting.

In mid-June, he and his troops were called to Richmond, Virginia, to help oppose McClellan's advance up the York-James peninsula. They served under Robert E Lee in the series of battles known as the Seven Days'Battles[?]. Jackson's performance in those battles is generally considered to be lackluster, for reasons that are disputed, though a severe lack of sleep after the grueling march from the Valley was probably a large factor.

Jackson was now a corps commander under Lee. At Second Battle of Bull Run, he helped to administer the Federals another defeat on the same grounds as in 1861. When Lee decided to invade the North, Jackson took Harpers Ferry, then hastened to join the rest of the army at Sharpsburg, where they fought McClellan in the battle of Antietam. The Confederate forces held their position, but the battle had been extremely bloody for both sides, and Lee took the Army of Northern Virginia back across the Potomac River, ending the invasion.

Jackson's troops held off a ferocious Union assault at Fredericksburg. At the Battle of Chancellorsville, Jackson's forces flanked the Union army, and in an intense battle deep in the tangled woods drove them back from their lines. Darkness ended the assault, and by bad luck Jackson and his staff were mistaken for a Union cavalry force by Confederate troops and fired upon. Jackson was hit by three bullets; his arm had to be amputated, and he died seven days later of complications from the wound.

Jackson is considered one of the great characters of the Civil War. He was profoundly religious, a deacon in the Presbyterian Church. He disliked fighting on Sunday, though that didn't stop him from doing so. He loved his wife very much and sent her tender letters. He generally wore old, worn-out clothes rather than a fancy uniform, and often looked more like a moth-eaten private than a corps commander. In command he was extremely secretive about his plans and extremely punctilious about military discipline. The South mourned his death; he was and still is greatly admired there. He is buried at VMI, and memorialized on Georgia's Stone Mountain[?] and in many other places.